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- PDB-9c9f: Crystal structures fluoroacetate dehalogenase D4B from Delftia ac... -

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Basic information

Entry
Database: PDB / ID: 9c9f
TitleCrystal structures fluoroacetate dehalogenase D4B from Delftia acidovorans strain D4B
ComponentsFluoroacetate dehalogenase
KeywordsTRANSFERASE / Dehalogenase PFAS
Function / homologyacylglycerol catabolic process / monoacylglycerol lipase activity / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / membrane / Alpha/beta hydrolase fold
Function and homology information
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCaputo, A.T. / Hu, M. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
Citation
Journal: To Be Published
Title: Crystal structures of two fluoroacetate dehalogenases
Authors: Hu, M. / Caputo, A.T. / Scott, C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
C: Fluoroacetate dehalogenase
D: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)143,2314
Polymers143,2314
Non-polymers00
Water12,899716
1
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)71,6162
Polymers71,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fluoroacetate dehalogenase
D: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)71,6162
Polymers71,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.936, 83.778, 84.917
Angle α, β, γ (deg.)101.598, 96.027, 94.673
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 52 or resid 54 through 298))
d_2ens_1(chain "B" and (resid 6 through 52 or resid 54 through 298))
d_3ens_1(chain "C" and (resid 6 through 52 or resid 54 through 298))
d_4ens_1(chain "D" and (resid 6 through 52 or resid 54 through 298))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TRPTRPPROPROAA6 - 5226 - 72
d_12LEULEUGLNGLNAA54 - 29874 - 318
d_21TRPTRPPROPROBB6 - 5226 - 72
d_22LEULEUGLNGLNBB54 - 29874 - 318
d_31TRPTRPPROPROCC6 - 5226 - 72
d_32LEULEUGLNGLNCC54 - 29874 - 318
d_41TRPTRPPROPRODD6 - 5226 - 72
d_42LEULEUGLNGLNDD54 - 29874 - 318

NCS oper:
IDCodeMatrixVector
1given(-0.980003924189, -0.1989557543, 0.00298603505332), (-0.197962290431, 0.976405269634, 0.0862767697433), (-0.0200808401642, 0.0839604505763, -0.996266732656)-0.632423747811, 0.173527025751, -0.338280525864
2given(-0.999699364247, -0.0244474665066, -0.00187149837987), (0.0244440643803, -0.999699543153, 0.00181965285455), (-0.00191542197758, 0.00177335877496, 0.999996593173)18.1186819121, 37.6066359803, 0.118992828188
3given(0.983917206226, 0.178345477245, 0.00999109801386), (0.178507143518, -0.979695599983, -0.0912783166284), (-0.006490840178, 0.0915937886531, -0.995775299389)18.7234964237, 37.4725937016, -0.300907055014

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Components

#1: Protein
Fluoroacetate dehalogenase


Mass: 35807.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Strain: D4B / Gene: Daci_4283 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BLX5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 14 mg/ml 25 %(w/v) Polyethylene glycol 3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.98→82.538 Å / Num. obs: 77693 / % possible obs: 97.6 % / Redundancy: 3 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.123 / Rrim(I) all: 0.22 / Net I/σ(I): 3
Reflection shellResolution: 1.98→2.016 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.315 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3823 / CC1/2: 0.31 / Rpim(I) all: 0.948 / Rrim(I) all: 1.63 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROC1.0.5data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→39.41 Å / SU ML: 0.2867 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.41
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 3777 4.89 %
Rwork0.2213 73385 -
obs0.2226 77162 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.11 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9393 0 0 716 10109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00539660
X-RAY DIFFRACTIONf_angle_d0.837513148
X-RAY DIFFRACTIONf_chiral_restr0.04351386
X-RAY DIFFRACTIONf_plane_restr0.01561751
X-RAY DIFFRACTIONf_dihedral_angle_d14.41423563
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.816228008579
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.659719381635
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.536038314913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.37791140.32672380X-RAY DIFFRACTION86.33
2.01-2.030.36711300.33132644X-RAY DIFFRACTION93.06
2.03-2.060.35331370.31912671X-RAY DIFFRACTION95.67
2.06-2.090.33131370.31152693X-RAY DIFFRACTION96.49
2.09-2.120.32151170.30252761X-RAY DIFFRACTION96.93
2.12-2.160.32591290.30422763X-RAY DIFFRACTION96.88
2.16-2.190.31491470.29362648X-RAY DIFFRACTION97.08
2.19-2.230.31091450.27562734X-RAY DIFFRACTION97.07
2.23-2.270.28881630.26262738X-RAY DIFFRACTION96.7
2.27-2.310.28711150.26482691X-RAY DIFFRACTION97.19
2.31-2.360.28771250.25622772X-RAY DIFFRACTION97.48
2.36-2.410.26631560.2462697X-RAY DIFFRACTION97.31
2.41-2.470.29021760.24462701X-RAY DIFFRACTION97.43
2.47-2.530.25771700.24782764X-RAY DIFFRACTION97.67
2.53-2.60.26881310.24212701X-RAY DIFFRACTION97.76
2.6-2.670.29681690.24792749X-RAY DIFFRACTION97.99
2.67-2.760.29751490.242694X-RAY DIFFRACTION97.66
2.76-2.860.29521290.23682776X-RAY DIFFRACTION97.68
2.86-2.970.24461380.22542713X-RAY DIFFRACTION98.38
2.97-3.110.22141170.21952818X-RAY DIFFRACTION97.96
3.11-3.270.24991560.20982708X-RAY DIFFRACTION97.61
3.27-3.480.241440.20752717X-RAY DIFFRACTION98.01
3.48-3.740.22391370.19082760X-RAY DIFFRACTION98.44
3.74-4.120.16231320.16862790X-RAY DIFFRACTION98.58
4.12-4.720.22321380.15842787X-RAY DIFFRACTION98.62
4.72-5.940.17811220.17882777X-RAY DIFFRACTION98.64
5.94-39.410.18031540.18462738X-RAY DIFFRACTION98.13

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